{ "_id": "6a1d29401d7bb097a0a385f3", "Package": "rtrees", "Title": "Deriving Phylogenies from Synthesis Trees", "Version": "2.0.2", "Authors@R": "person(given = \"Daijiang\",\nfamily = \"Li\",\nrole = c(\"aut\", \"cre\"),\nemail = \"daijianglee@gmail.com\",\ncomment = c(ORCID = \"0000-0002-0925-3421\"))", "Description": "Provides tools to derive species-level phylogenies from\nlarge synthesis mega-trees for a wide range of taxonomic\ngroups, including plants, birds, mammals, amphibians, reptiles,\nfish, bees, butterflies, and sharks. When a queried species is\nabsent from the mega-tree, it is grafted onto the tree using\none of two placement strategies: attachment at the basal node\nof the most closely related genus or family ('at_basal_node'),\nor random attachment below that basal node with probability\nproportional to branch length ('random_below_basal'). See Li\n(2023) for details. Multiple species\nfrom a genus not represented in the mega-tree are placed as a\npolytomy to preserve clade coherence. The package interfaces\nwith the 'megatrees' data package, which bundles or downloads\non demand curated mega-trees. Users can also provide their own\nmega-trees.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "URL": "https://daijiang.github.io/rtrees/", "VignetteBuilder": "knitr, R.rsp", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev", "Repository": "https://daijiang.r-universe.dev", "Date/Publication": "2026-06-01 02:17:30 UTC", "RemoteUrl": "https://github.com/daijiang/rtrees", "RemoteRef": "HEAD", "RemoteSha": "b786f81708d1039028805c76eaf2d642ae23e2fb", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-01 06:33:24 UTC", "User": "root" }, "Author": "Daijiang Li [aut, cre] (ORCID: )", "Maintainer": "Daijiang Li ", "MD5sum": "b866287feb0e10f1b5c344d1ecb0205d", "_user": "daijiang", "_type": "src", "_file": "rtrees_2.0.2.tar.gz", "_fileid": "c627ea3fe5b3e96f7e109f99f77c1c4162e145c0c692050861fc4854f623b1b2", "_filesize": 1985566, "_sha256": "c627ea3fe5b3e96f7e109f99f77c1c4162e145c0c692050861fc4854f623b1b2", "_created": "2026-06-01T06:33:24.000Z", "_published": "2026-06-01T06:40:00.377Z", "_distro": "noble", "_jobs": [ { "job": 78798699600, "time": 208, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7324858350" }, { "job": 78798699618, "time": 217, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7324860362" }, { "job": 78798699619, "time": 190, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7324854494" }, { "job": 78798699608, "time": 185, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7324853342" }, { "job": 78798699629, "time": 141, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7324848760" }, { "job": 78798699611, "time": 329, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7324893655" }, { "job": 78798699617, "time": 138, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7324844702" }, { "job": 78798699613, "time": 276, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7324881101" }, { "job": 78798331116, "time": 200, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7324811406" }, { "job": 78798699624, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7324839676" }, { "job": 78798699609, "time": 185, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7324853574" }, { "job": 78798699612, "time": 213, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7324859644" }, { "job": 78798699606, "time": 239, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7324865812" } ], "_buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/daijiang/rtrees", "_commit": { "id": "b786f81708d1039028805c76eaf2d642ae23e2fb", "author": "daijiang ", "committer": "daijiang ", "message": "re submit to CRAN\n", "time": 1780280250 }, "_maintainer": { "name": "Daijiang Li", "email": "daijianglee@gmail.com", "login": "daijiang", "description": "", "uuid": 1696911, "orcid": "0000-0002-0925-3421" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "ape", "role": "Imports" }, { "package": "tidytree", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "castor", "role": "Imports" }, { "package": "furrr", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "megatrees", "version": ">= 0.1.3", "role": "Imports" }, { "package": "fastmatch", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "piggyback", "role": "Suggests" }, { "package": "R.rsp", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "daijiang", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-32", "n": 4 }, { "week": "2026-11", "n": 1 }, { "week": "2026-18", "n": 4 }, { "week": "2026-20", "n": 2 }, { "week": "2026-21", "n": 9 }, { "week": "2026-22", "n": 3 }, { "week": "2026-23", "n": 1 } ], "_tags": [], "_topics": [ "phylogenetic-trees", "cpp" ], "_stars": 36, "_contributors": [ { "user": "daijiang", "count": 108, "uuid": 1696911 } ], "_userbio": { "uuid": 1696911, "type": "user", "name": "Daijiang Li" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rtrees" }, "_devurl": "https://github.com/daijiang/rtrees", "_pkgdown": "https://daijiang.github.io/rtrees/", "_searchresults": 91, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/rtrees.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "add_root_info", "bind_tip", "get_graft_status", "get_one_tree", "get_tree", "rm_stars", "sp_list_df" ], "_datasets": [ { "name": "classifications", "title": "Classifications of species", "object": "classifications", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "genus", "family", "taxon" ], "rows": 54580, "table": true, "tojson": true }, { "name": "taxa_supported", "title": "Taxonomic groups supported", "object": "taxa_supported", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "add_root_info", "title": "Add genus and family basal/root node information to a phylogeny", "topics": [ "add_root_info" ] }, { "page": "bind_tip", "title": "Bind a tip to a phylogeny", "topics": [ "bind_tip" ] }, { "page": "bind_tip_df", "title": "Bind a tip to a phylogeny (data frame version)", "topics": [ "bind_tip_df" ] }, { "page": "classifications", "title": "Classifications of species", "topics": [ "classifications" ] }, { "page": "get_graft_status", "title": "Extract grafting status information as a data frame", "topics": [ "get_graft_status" ] }, { "page": "get_one_tree", "title": "Derive a phylogeny from a mega-tree", "topics": [ "get_one_tree" ] }, { "page": "get_tree", "title": "Get one or multiple trees from megatree(s)", "topics": [ "get_tree" ] }, { "page": "rm_stars", "title": "Remove trailing *", "topics": [ "rm_stars" ] }, { "page": "sp_list_df", "title": "Convert a vector of species names to a data frame", "topics": [ "sp_list_df" ] }, { "page": "taxa_supported", "title": "Taxonomic groups supported", "topics": [ "taxa_supported" ] } ], "_readme": "https://github.com/daijiang/rtrees/raw/HEAD/README.md", "_rundeps": [ "ape", "castor", "cli", "codetools", "cpp11", "data.table", "digest", "dplyr", "fastmatch", "fs", "furrr", "future", "generics", "globals", "glue", "jsonlite", "lattice", "lazyeval", "lifecycle", "listenv", "magrittr", "Matrix", "megatrees", "naturalsort", "nlme", "parallelly", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "Rcpp", "RcppEigen", "rlang", "RSpectra", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tidytree", "utf8", "vctrs", "withr", "yulab.utils" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "grafting_scenarios.html.asis", "filename": "grafting_scenarios.html", "title": "grafting_scenarios", "engine": "R.rsp::asis", "headings": [], "created": "2026-05-25 16:14:09", "modified": "2026-05-25 16:14:09", "commits": 1 }, { "source": "Non-monophyletic-groups.html.asis", "filename": "Non-monophyletic-groups.html", "title": "Non-monophyletic-groups", "engine": "R.rsp::asis", "headings": [], "created": "2026-05-25 16:14:09", "modified": "2026-05-25 16:14:09", "commits": 1 }, { "source": "Simple_example.html.asis", "filename": "Simple_example.html", "title": "Simple_example", "engine": "R.rsp::asis", "headings": [], "created": "2026-05-18 15:09:56", "modified": "2026-05-18 15:09:56", "commits": 1 }, { "source": "speed.Rmd", "filename": "speed.html", "title": "Speed comparisons", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-01-03 22:34:01", "modified": "2026-05-18 19:54:20", "commits": 6 } ], "_score": 6.661471928766619, "_indexed": true, "_nocasepkg": "rtrees", "_universes": [ "daijiang" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.0.2", "date": "2026-06-01T06:36:04.000Z", "distro": "noble", "arch": "aarch64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "d8ecd1d8d22fe1b1d38c1eac92657a0863e3d0fc5f3ce133acb3b77ca66399c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.7.0", "os": "linux", "version": "2.0.2", "date": "2026-06-01T06:36:04.000Z", "distro": "noble", "arch": "x86_64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "d407a3fc4bb6514a55761c035370ce849534c671600dfa32cd2350856183902f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.6.0", "os": "linux", "version": "2.0.2", "date": "2026-06-01T06:35:48.000Z", "distro": "noble", "arch": "aarch64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "2c8f55f97cfb5089e620f23c69461bcdf70fce32846e545532f8d1efe7fffbbd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.6.0", "os": "linux", "version": "2.0.2", "date": "2026-06-01T06:35:38.000Z", "distro": "noble", "arch": "x86_64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "08a8b19801b108eca0e1368c574b74920f84e787de5198d6ca1ff6a3d3287b10", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.5.3", "os": "mac", "version": "2.0.2", "date": "2026-06-01T06:35:29.000Z", "arch": "aarch64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "a372665111ec0c5ce0ed5b2176eb345b9a5ad954f619337bc02cb451d7e973f8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.5.3", "os": "mac", "version": "2.0.2", "date": "2026-06-01T06:36:56.000Z", "arch": "x86_64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "9b63ecc9dc7d636c073d7a4dbeba0dca6f3130c9ed317e83160e5ca82899b633", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.6.0", "os": "mac", "version": "2.0.2", "date": "2026-06-01T06:35:11.000Z", "arch": "aarch64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "95fbcaeb57d98648a199fb8e5f965865c4987ec9fd885071df78ec345bd6d402", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.6.0", "os": "mac", "version": "2.0.2", "date": "2026-06-01T06:36:47.000Z", "arch": "x86_64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "6018f44a979924c39985c91cd62f779184c3cf3b8461ff446a633a2d51120f37", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.6.0", "os": "wasm", "version": "2.0.2", "date": "2026-06-01T06:35:50.000Z", "arch": "emscripten", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "2d63f026c9a9280cbd021ccb4a1b389dc17b516b03c902abbc9cf44dc9d0d260", "status": "success", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.7.0", "os": "win", "version": "2.0.2", "date": "2026-06-01T06:34:55.000Z", "arch": "x86_64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "dfccb4264c06508593c72f45be8b4cfbc029305cb36086c3807e77f2be30d4ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.5.3", "os": "win", "version": "2.0.2", "date": "2026-06-01T06:34:50.000Z", "arch": "x86_64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "ebc431ff02385f6e62922c281f7f8671f9f18eb488c5c9e9556abb440fdb4a12", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" }, { "r": "4.6.0", "os": "win", "version": "2.0.2", "date": "2026-06-01T06:35:37.000Z", "arch": "x86_64", "commit": "b786f81708d1039028805c76eaf2d642ae23e2fb", "fileid": "e5f93157f5ee98f10f50fe420d0068960fe751cf37e9be3fd78fc72267ee6e72", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/daijiang/actions/runs/26736282226" } ] }